#!/bin/sh -
unset -v file arg1 arg2
while getopts a:b:i: option
do
  case "${option}" in
    (a) arg1=${OPTARG};;
    (b) arg2=${OPTARG};;
    (i) file=${OPTARG};;
    (*) exit 1;;
  esac
done

shift "$((OPTIND - 1))"
# now "$@" contains the rest of the arguments

if [ -z "${file+set}" ]; then
  if [ "$#" -eq 0 ]; then
    echo >&2 "No input file specified"
    exit 1
  else
    file=$1 # first non-option argument
    shift
  fi
fi

I changed the bash to sh as there's nothing bash-specific in that code.

#!/bin/sh - 

# Beware variables can be inherited from the environment. So
# it's important to start with a clean slate if you're going to
# dereference variables while not being guaranteed that they'll
# be assigned to:
unset -v file arg1 arg2

# no need to initialise OPTIND here as it's the first and only
# use of getopts in this script and sh should already guarantee it's
# initialised.
while getopts a:b:i: option
do
  case "${option}" in
    (a) arg1=${OPTARG};;
    (b) arg2=${OPTARG};;
    (i) file=${OPTARG};;
    (*) exit 1;;
  esac
done

shift "$((OPTIND - 1))"
# now "$@" contains the rest of the arguments

if [ -z "${file+set}" ]; then
  if [ "$#" -eq 0 ]; then
    echo >&2 "No input file specified"
    exit 1
  else
    file=$1 # first non-option argument
    shift
  fi
fi

if [ "$#" -gt 0 ]; then
  echo There are more arguments:
  printf ' - "%s"\n' "$@"
fi

I changed the bash to sh as there's nothing bash-specific in that code.